Todd H Oakley

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc The origins of novel protein interactions during animal opsin evolution
    David C Plachetzki
    Ecology, Evolution and Marine Biology, University of California at Santa Barbara, Santa Barbara, California, United States of America
    PLoS ONE 2:e1054. 2007
  2. doi request reprint Phylotranscriptomics to bring the understudied into the fold: monophyletic ostracoda, fossil placement, and pancrustacean phylogeny
    Todd H Oakley
    Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
    Mol Biol Evol 30:215-33. 2013
  3. pmc Repression and loss of gene expression outpaces activation and gain in recently duplicated fly genes
    Todd H Oakley
    Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
    Proc Natl Acad Sci U S A 103:11637-41. 2006
  4. ncbi request reprint Differential expression of duplicated opsin genes in two eyetypes of ostracod crustaceans
    Todd H Oakley
    Biology Department, Duke University, Durham, NC 27706, USA
    J Mol Evol 59:239-49. 2004
  5. ncbi request reprint Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data
    Todd H Oakley
    Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 22:40-50. 2005
  6. ncbi request reprint Today's multiple choice exam: (a) gene duplication; (b) structural mutation; (c) co-option; (d) regulatory mutation; (e) all of the above
    Todd H Oakley
    University of California Santa Barbara
    Evol Dev 9:523-4. 2007
  7. doi request reprint Genomics and the evolutionary origins of nervous system complexity
    Todd H Oakley
    Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
    Curr Opin Genet Dev 18:479-92. 2008
  8. ncbi request reprint Furcation, field-splitting, and the evolutionary origins of novelty in arthropod photoreceptors
    Todd H Oakley
    Ecology Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
    Arthropod Struct Dev 36:386-400. 2007
  9. pmc Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach
    Ajna S Rivera
    University of California Santa Barbara, 93106, USA
    BMC Evol Biol 10:123. 2010
  10. ncbi request reprint Erratic rates of molecular evolution and incongruence of fossil and molecular divergence time estimates in Ostracoda (Crustacea)
    Oive Tinn
    Ecology Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
    Mol Phylogenet Evol 48:157-67. 2008

Detail Information

Publications32

  1. pmc The origins of novel protein interactions during animal opsin evolution
    David C Plachetzki
    Ecology, Evolution and Marine Biology, University of California at Santa Barbara, Santa Barbara, California, United States of America
    PLoS ONE 2:e1054. 2007
    ..Biologists are gaining an increased understanding of the genetic bases of phenotypic change during evolution. Nevertheless, the origins of phenotypes mediated by novel protein-protein interactions remain largely undocumented...
  2. doi request reprint Phylotranscriptomics to bring the understudied into the fold: monophyletic ostracoda, fossil placement, and pancrustacean phylogeny
    Todd H Oakley
    Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
    Mol Biol Evol 30:215-33. 2013
    ....
  3. pmc Repression and loss of gene expression outpaces activation and gain in recently duplicated fly genes
    Todd H Oakley
    Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
    Proc Natl Acad Sci U S A 103:11637-41. 2006
    ..The trend is important because repression of gene expression is a hypothesized mechanism for the origin of evolutionarily novel morphologies through specialization...
  4. ncbi request reprint Differential expression of duplicated opsin genes in two eyetypes of ostracod crustaceans
    Todd H Oakley
    Biology Department, Duke University, Durham, NC 27706, USA
    J Mol Evol 59:239-49. 2004
    ..Why ostracods may have retained multiple recent opsin gene duplicates is unknown, but we discuss several possible hypotheses...
  5. ncbi request reprint Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data
    Todd H Oakley
    Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 22:40-50. 2005
    ..The comparative methods presented here are general enough to test a wide range of evolutionary hypotheses using genomic-scale data from any organism...
  6. ncbi request reprint Today's multiple choice exam: (a) gene duplication; (b) structural mutation; (c) co-option; (d) regulatory mutation; (e) all of the above
    Todd H Oakley
    University of California Santa Barbara
    Evol Dev 9:523-4. 2007
  7. doi request reprint Genomics and the evolutionary origins of nervous system complexity
    Todd H Oakley
    Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
    Curr Opin Genet Dev 18:479-92. 2008
    ..These examples illustrate that while a variety of different mechanisms increase biological complexity, they can be understood in a generalized comparative framework...
  8. ncbi request reprint Furcation, field-splitting, and the evolutionary origins of novelty in arthropod photoreceptors
    Todd H Oakley
    Ecology Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
    Arthropod Struct Dev 36:386-400. 2007
    ..These studies provide a new perspective on the evolution of arthropod photoreceptors and provide a comparative approach that generalizes to the study of any evolutionary novelty...
  9. pmc Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach
    Ajna S Rivera
    University of California Santa Barbara, 93106, USA
    BMC Evol Biol 10:123. 2010
    ....
  10. ncbi request reprint Erratic rates of molecular evolution and incongruence of fossil and molecular divergence time estimates in Ostracoda (Crustacea)
    Oive Tinn
    Ecology Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
    Mol Phylogenet Evol 48:157-67. 2008
    ..Our results illustrate the difficulty in consistently estimating lineage divergence times, even in the presence of a voluminous fossil record...
  11. doi request reprint Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history
    Marc W Cadotte
    National Center for Ecological Analysis and Synthesis, University of California, 735 State St, Santa Barbara, CA 93101, USA
    Ecol Lett 13:96-105. 2010
    ..We compare these new metrics to existing ones, and use them to explore diversity patterns in a typical California annual grassland plant community at the Jasper Ridge biological preserve...
  12. pmc Evolutionary history and the effect of biodiversity on plant productivity
    Marc W Cadotte
    National Center for Ecological Analysis and Synthesis, University of California, 735 State Street, Santa Barbara, CA 93101, USA
    Proc Natl Acad Sci U S A 105:17012-7. 2008
    ..Our results reveal how evolutionary history can provide critical information for understanding, predicting, and potentially ameliorating the effects of biodiversity loss and should serve as an impetus for new biodiversity experiments...
  13. ncbi request reprint Ontogeny of sexual dimorphism via tissue duplication in an ostracod (Crustacea)
    Ajna S Rivera
    Marine Science Institute, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
    Evol Dev 11:233-43. 2009
    ..Depending on the evolutionary history of the duplicated field, it may have either facilitated or directly caused the observed sexual dimorphism of philomedid ostracods...
  14. pmc A post-synaptic scaffold at the origin of the animal kingdom
    Onur Sakarya
    Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, United States of America
    PLoS ONE 2:e506. 2007
    ....
  15. doi request reprint Evasion of predators contributes to the maintenance of male eyes in sexually dimorphic Euphilomedes ostracods (Crustacea)
    Daniel I Speiser
    Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106 9620, USA
    Integr Comp Biol 53:78-88. 2013
    ..The presence of suites of eye regulatory genes in our Euphilomedes juvenile male transcriptome will allow us, in future studies, to test how ostracods regulate the development of their sexually dimorphic eyes. ..
  16. pmc The Amphimedon queenslandica genome and the evolution of animal complexity
    Mansi Srivastava
    Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Nature 466:720-6. 2010
    ..Notably, many of the genes associated with the emergence of animals are also implicated in cancer, which arises from defects in basic processes associated with metazoan multicellularity...
  17. pmc The evolution of phototransduction from an ancestral cyclic nucleotide gated pathway
    David C Plachetzki
    Department of Ecology, Evolution and Marine Biology, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
    Proc Biol Sci 277:1963-9. 2010
    ..g. fly and mollusc) vision...
  18. doi request reprint Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae
    Markos A Alexandrou
    Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
    Mol Phylogenet Evol 69:514-23. 2013
    ..Our study represents the first attempt to estimate the absolute timing of a complex behavioral trait in relation to a genome duplication event...
  19. doi request reprint Dispersal between shallow and abyssal seas and evolutionary loss and regain of compound eyes in cylindroleberidid ostracods: conflicting conclusions from different comparative methods
    Anna E Syme
    Ecology, Evolution, Marine Biology and Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
    Syst Biol 61:314-36. 2012
    ....
  20. doi request reprint Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony
    Onur Sakarya
    Department of Computer Science, University of California, Santa Barbara, CA 93106, USA
    Bioinformatics 24:606-12. 2008
    ....
  21. ncbi request reprint Understanding the dermal light sense in the context of integrative photoreceptor cell biology
    M Desmond Ramirez
    Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California 93106, USA
    Vis Neurosci 28:265-79. 2011
    ..Our new classification scheme, combined with modern investigative techniques, will help us address these hypotheses in great detail and generate new hypothesis regarding the function and evolution of dispersed photoreceptor cells...
  22. pmc A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment
    Annie R Lindgren
    Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, 93106, USA
    BMC Evol Biol 12:129. 2012
    ..We then create a character matrix of habitat type and morphological characters, which we use to infer ancestral character states and test for correlation between habitat and morphology...
  23. pmc The new biology: beyond the Modern Synthesis
    Michael R Rose
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Biol Direct 2:30. 2007
    ..The foundations of that "Modernist" biology had thus largely crumbled by the start of the 21st Century. This in turn raises the question of foundations for biology in the 21st Century...
  24. pmc Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye
    Todd H Oakley
    Department of Biology, Duke University, Box 90325, Durham, NC 27708 0325, USA
    Proc Natl Acad Sci U S A 99:1426-30. 2002
    ..Either compound eyes with detailed similarities evolved multiple times in different arthropod groups or compound eyes have been lost in a seemingly inordinate number of arthropod lineages...
  25. doi request reprint Type II opsins: evolutionary origin by internal domain duplication?
    Nicholas D Larusso
    Department of Computer Science, University of California, Santa Barbara, CA 93106, USA
    J Mol Evol 66:417-23. 2008
    ..This convergence may indicate an important role for seven-TM protein structure for retinal-based light sensitivity...
  26. ncbi request reprint Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology
    Jeanne M Serb
    Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, USA
    Bioessays 27:1158-66. 2005
    ..We argue that this application of "hierarchical phylogenetics" can be a unifying analytical approach to the field of EDB...
  27. doi request reprint The evolution of complexity in the visual systems of stomatopods: insights from transcriptomics
    Megan L Porter
    Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
    Integr Comp Biol 53:39-49. 2013
    ....
  28. ncbi request reprint Key transitions during the evolution of animal phototransduction: novelty, "tree-thinking," co-option, and co-duplication
    David C Plachetzki
    Ecology, Evolution and Marine Biology The University of California Santa Barbara, CA 93106
    Integr Comp Biol 47:759-69. 2007
    ....
  29. pmc Ocular and extraocular expression of opsins in the rhopalium of Tripedalia cystophora (Cnidaria: Cubozoa)
    Jan Bielecki
    Ecology, Evolution and Marine Biology, University of California at Santa Barbara, Santa Barbara, California, United States of America
    PLoS ONE 9:e98870. 2014
    ..Tc-neo is expressed in a confined part of the neuropil and is probably involved in extraocular light sensation, presumably in relation to diurnal activity. ..
  30. pmc Shared ancestry influences community stability by altering competitive interactions: evidence from a laboratory microcosm experiment using freshwater green algae
    Patrick A Venail
    School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI 48109 1041, USA
    Proc Biol Sci 280:20131548. 2013
    ..As such, patterns of shared ancestry may help us predict the ecosystem-level consequences of biodiversity loss. ..
  31. pmc Using phylogenetic, functional and trait diversity to understand patterns of plant community productivity
    Marc W Cadotte
    National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
    PLoS ONE 4:e5695. 2009
    ..Thus, understanding phenotypic attributes that allow species to partition resources is fundamentally important to explaining diversity-productivity relationships...